# HG changeset patch
# User fubar
# Date 1393469385 18000
# Node ID b21cd7bec41fc0852244c5a09ab91ed768edd36a
# Parent  f86cb6b724ee1dc4dba2eeb43ca750bfc62b7131
Uploaded

diff -r f86cb6b724ee -r b21cd7bec41f rgedgeRpaired_nocamera.xml
--- a/rgedgeRpaired_nocamera.xml	Wed Feb 26 01:50:06 2014 -0500
+++ b/rgedgeRpaired_nocamera.xml	Wed Feb 26 21:49:45 2014 -0500
@@ -758,9 +758,10 @@
          DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
          DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
          }
-      norm.factor = calcNormFactors(DGEList)
+      calcNormFactors(DGEList) # -> object$samples$norm.factors
+      ls = colSums(DGEList$counts) * DGEList$samples$norm.factors
       pdf("VOOM_mean_variance_plot.pdf")
-      dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor)
+      dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = ls)
       dev.off()
       # Use limma to fit data
       fit = lmFit(dat.voomed, mydesign)